Contacts of the helix formed by residues 168 - 175 (chain A) in PDB entry 1W57
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 168 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76A ARG* 4.0 10.5 - - - +
80A LEU* 6.0 0.2 - - - -
145A ILE* 3.7 14.1 - - + +
146A GLN 5.5 0.7 - - - +
147A THR* 5.8 0.9 - - - +
149A GLN* 3.2 19.7 + - - +
166A PHE* 3.6 4.4 - - - +
167A THR* 1.3 80.7 + - - +
169A ASP* 1.3 64.7 + - - +
170A SER* 2.6 36.0 + - - -
171A THR* 2.7 45.7 + - - +
172A ALA* 3.5 8.5 + - - +
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Residues in contact with ASP 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A ARG* 3.6 6.8 + - - -
80A LEU* 3.1 24.0 - - - +
94A VAL* 3.1 33.6 - - - +
119A CYS* 4.1 2.9 - - - -
149A GLN* 2.8 25.6 + - + +
151A SER* 3.7 21.2 + - - +
156A LEU* 3.6 23.6 - - + +
168A ASP* 1.3 71.4 - - - +
170A SER* 1.3 61.9 + - - +
172A ALA* 3.3 4.4 + - - +
173A ILE* 3.0 26.9 + - - +
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Residues in contact with SER 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A CYS* 3.6 21.1 - - - -
121A THR* 4.3 6.8 - - - +
145A ILE* 4.3 10.2 - - - +
149A GLN* 3.8 7.3 + - - -
168A ASP* 2.6 28.2 + - - -
169A ASP* 1.3 74.4 - - - +
171A THR* 1.3 62.3 + - - +
173A ILE 3.3 0.3 + - - -
174A ALA* 2.8 31.5 + - - +
180A ILE* 3.4 24.8 - - - +
182A PHE* 5.2 3.1 - - - -
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Residues in contact with THR 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A ILE* 6.3 2.5 - - + -
166A PHE* 3.9 15.2 - - - +
167A THR* 4.3 6.6 + - - +
168A ASP* 2.7 35.3 + - - +
170A SER* 1.3 85.5 + - - +
172A ALA* 1.3 57.2 + - - +
174A ALA* 3.7 7.7 - - - +
175A ALA* 2.9 32.7 + - - +
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Residues in contact with ALA 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A LEU* 4.6 3.8 - - + -
159A ALA* 3.7 18.1 - - + +
160A LEU* 4.1 14.8 - - + -
166A PHE* 3.5 37.1 - - + -
168A ASP 3.5 7.8 + - - +
169A ASP* 3.3 11.0 + - - +
170A SER 3.2 0.4 - - - -
171A THR* 1.3 80.2 + - - +
173A ILE* 1.3 66.3 + - - +
175A ALA* 3.4 8.5 + - - +
176A MET* 3.6 8.3 + - - +
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Residues in contact with ILE 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A ASP* 3.8 26.7 - - + +
119A CYS* 3.8 14.6 - - + -
151A SER* 4.6 6.5 - - - +
152A LYS 4.8 0.4 - - - +
155A LEU* 3.8 19.5 - - + +
156A LEU* 3.6 46.2 - - + +
159A ALA* 4.2 4.0 - - + -
169A ASP 3.0 20.3 + - - +
172A ALA* 1.3 74.3 - - - +
174A ALA* 1.3 61.4 + - - +
176A MET* 3.2 10.7 + - - +
178A GLY* 3.2 27.9 + - - -
180A ILE* 3.7 22.2 - - + -
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Residues in contact with ALA 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A SER 2.8 18.9 + - - +
171A THR* 3.7 8.7 - - - +
173A ILE* 1.3 72.7 - - - +
175A ALA* 1.3 57.3 + - - +
176A MET 3.0 4.9 - - - -
177A GLY* 3.0 21.3 + - - -
178A GLY 3.8 11.7 - - - +
180A ILE* 3.9 14.6 - - + +
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Residues in contact with ALA 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A PHE* 3.8 26.7 - - + -
171A THR 2.9 19.7 + - - +
172A ALA 4.0 1.3 - - - +
173A ILE 3.4 0.4 - - - -
174A ALA* 1.3 74.2 - - - +
176A MET* 1.3 60.4 + - - +
177A GLY 3.5 0.7 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il